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Merge pull request #261 from RobertGawron/feature/rev_5_0 

Feature/rev 5 0
pull/263/head
Robert 2021-08-07 17:37:46 +02:00 zatwierdzone przez GitHub
rodzic 1d374f2c4f 50cfdd06e3
commit f562f8569c
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13
Documentation/Diagrams/UARTFrameFormat.tex
Wyświetl plik

@ -25,20 +25,21 @@ long/.style={short,text width=60pt}
\node (StartPoint) [text depth=13pt, text height=6pt]{};
\shnode{StartPoint}{MsgId}{msg id};
\shnode{MsgId}{MsgLen}{msg length};
\lnode{MsgLen}{Configuration}{ADC configuration};
\shnode{StartPoint}{MsgType}{msg type};
\shnode{MsgType}{MsgLen}{msg length};
\lnode{MsgLen}{MsgCounter}{msg \\ counter};
\lnode{MsgCounter}{Configuration}{ADC configuration};
\lnode{Configuration}{MSBADC}{MSB ADC value};
\lnode{MSBADC}{LSBADC}{LSB ADC value};
\lnode{LSBADC}{CRC}{CRC};
\draw[decorate,decoration={brace,raise=3pt}] (MsgId.north west) -- node[above=4pt] {Preamble} (MsgLen.north east);
\draw[decorate,decoration={brace,raise=3pt}] (MsgType.north west) -- node[above=4pt] {Preamble} (MsgCounter.north east);
\draw[decorate,decoration={brace,raise=3pt}] (Configuration.north west) -- node[above=4pt] {Data} (LSBADC.north east);
\draw[decorate,decoration={brace,raise=3pt}] (CRC.north west) -- node[above=4pt] {CRC} (CRC.north east);
\draw (MsgId.south west) -- +(0,-1.2cm);
\draw (MsgType.south west) -- +(0,-1.2cm);
\draw (MsgLen.south east) -- +(0,-1.2cm);
\draw[<->] ( $ (MsgId.south west) +(0,-0.6cm) $ ) -- node[fill=white] {1 Byte} ( $ (MsgLen.south east) +(0,-0.6cm) $ );
\draw[<->] ( $ (MsgType.south west) +(0,-0.6cm) $ ) -- node[fill=white] {1 byte} ( $ (MsgLen.south east) +(0,-0.6cm) $ );
\end{tikzpicture}

11
Simulation/hardware_connection.py
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@ -1,11 +0,0 @@
class HardwareConnection:
def __init__(self, config):
pass
def connect(self):
pass
def getMeasurement(self):
return [1, 2, 3, 4, 5]

6
Simulation/main.py
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@ -1,13 +1,13 @@
import sys
sys.path.append('../Software/DataAcquisition')
from hardware_connection import HardwareConnection # noqa: E402
from physical_layer import PhysicalLayer # noqa: E402
from state_machine import IonizationChamberStateMachine # noqa: E402
import config # noqa: E402
if __name__ == "__main__":
hardware = HardwareConnection(config)
machine = IonizationChamberStateMachine(hardware)
physicalLayer = PhysicalLayer(config)
machine = IonizationChamberStateMachine(physicalLayer)
while True:
machine.tick()

11
Simulation/physical_layer.py 100644
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@ -0,0 +1,11 @@
class PhysicalLayer:
def __init__(self, config):
pass
def connect(self):
pass
def getData(self):
return [1, 2, 3, 4, 5, 9]

52
Software/DataAcquisition/README.md
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@ -1,15 +1,41 @@
# Firmware
## Setting up development environment on Linux
## Setup
1. Install tools via apt-get:
* [Setting up development environment on Linux
](https://github.com/RobertGawron/IonizationChamber/wiki/Setting-up-development-environment-on-Linux)
```console
apt-get install screen git sdcc doxygen uncrustify libusb-1.0-0-dev python3-pip texlive-latex-base texlive-latex-extra texlive-extra-utils poppler-utils cmake cppcheck r-base-core shellcheck
```
3. Install python libraries.
```console
pip3 install pyserial
pip3 install flake8 flake8-html
```
## Architecture
4. Install R libraries, run R in command line:
```console
pi@raspberrypi:~/IonizationChamber/software/DataAcquisitionFromDevice $ R
R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: arm-unknown-linux-gnueabihf (32-bit)
```
Type (write yes on next prompts):
```
install.packages('latticeExtra')
```
```
install.packages('gridExtra')
```
```
install.packages('Hmisc')
```
<img src="../../Documentation/Diagrams/HostArchitecture.svg" width="100%">
## Collecting measurements
@ -17,9 +43,9 @@
2. **Run data acquisition script**, it will log Ionization Chamber output on the screen and also it will save it to data.csv for further processing.
```python main.py```
3. When all data is logged, terminate ```python main.py``.
```
python main.py
```
## Plotting signal value in domain time + plotting histogram
@ -27,7 +53,9 @@ This mode is useful to look on measurement changes over time.
After collecting data run script to post-process it and generate diagrams:
```Rscript main.R```
```
Rscript main.R
```
A new .png image with timestamp in its name will be created in directory where script is.
@ -42,7 +70,9 @@ Below is example of such generated plot.
2. Edit ```boxplot.R```, to match filenames of .cvs files and labels of measurements.
3. Run:
```Rscript boxplot.R```
```
Rscript boxplot.R
```
A new .png image with timestamp in its name will be created in directory where script is.

45
Software/DataAcquisition/application_layer.py 100644
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@ -0,0 +1,45 @@
from transport_layer import TransportLayer
from enum import Enum
class ADC_RESOLUTION(Enum):
R12 = 1
R13 = 2
R14 = 3
def convert(upperByte, lowerByte, resolution):
"""
based on https://ww1.microchip.com/downloads/en/DeviceDoc/22072b.pdf
assumed that gain = 1
"""
def digitalToAnalog(value, lsb, pga):
return (value * (lsb / pga))
digitalOutput = (upperByte << 8) | lowerByte
if resolution == ADC_RESOLUTION.R12:
return digitalToAnalog(digitalOutput, (1 * 0.01), 1)
if resolution == ADC_RESOLUTION.R13:
return digitalToAnalog(digitalOutput, (250 * 0.0000001), 1)
if resolution == ADC_RESOLUTION.R14:
return digitalToAnalog(digitalOutput, (62.5 * 0.000001), 1)
class ApplicationLayer:
def __init__(self, physicalLayer):
self.transportLayer = TransportLayer(physicalLayer)
def connect(self):
self.transportLayer.connect()
def getMeasurement(self):
dataIn = self.transportLayer.getFrame()
(msb, lsb) = (dataIn[2], dataIn[3])
deviceMeasurement = convert(
msb, lsb, ADC_RESOLUTION.R14)
return deviceMeasurement

19
Software/DataAcquisition/ionization_chamber.py
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@ -1,19 +0,0 @@
import mcp3425
class IonizationChamber:
def __init__(self, ionizationSensor):
self.ionizationSensor = ionizationSensor
def connect(self):
self.ionizationSensor.connect()
def getMeasurement(self):
dataIn = self.ionizationSensor.getMeasurement()
(msb, lsb) = (dataIn[2], dataIn[3])
deviceMeasurement = mcp3425.convert(
msb, lsb, mcp3425.MCP3425_RESOLUTION.R14)
return deviceMeasurement

6
Software/DataAcquisition/main.py
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@ -1,11 +1,11 @@
from hardware_connection import HardwareConnection
from physical_layer import PhysicalLayer
from state_machine import IonizationChamberStateMachine
import config
if __name__ == "__main__":
hardware = HardwareConnection(config)
machine = IonizationChamberStateMachine(hardware)
physicalLayer = PhysicalLayer(config)
machine = IonizationChamberStateMachine(physicalLayer)
while True:
machine.tick()

27
Software/DataAcquisition/mcp3425.py
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@ -1,27 +0,0 @@
"""
based on https://ww1.microchip.com/downloads/en/DeviceDoc/22072b.pdf
assumed that gain = 1
"""
from enum import Enum
class MCP3425_RESOLUTION(Enum):
R12 = 1
R13 = 2
R14 = 3
def convert(upperByte, lowerByte, resolution):
def digitalToAnalog(value, lsb, pga):
return (value * (lsb / pga))
digitalOutput = (upperByte << 8) | lowerByte
if resolution == MCP3425_RESOLUTION.R12:
return digitalToAnalog(digitalOutput, (1 * 0.01), 1)
if resolution == MCP3425_RESOLUTION.R13:
return digitalToAnalog(digitalOutput, (250 * 0.0000001), 1)
if resolution == MCP3425_RESOLUTION.R14:
return digitalToAnalog(digitalOutput, (62.5 * 0.000001), 1)

15
Software/DataAcquisition/measurement_storage.py 100644
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@ -0,0 +1,15 @@
import csv
class MeasurementStorage:
def __init__(self):
self.CVS_FileName = "data.csv"
self.CVS_Header = ['Time', 'Counter']
def connect(self):
CVS_Handler = open(self.CVS_FileName, 'w', encoding='UTF8', newline='')
self.CVS_Writter = csv.writer(CVS_Handler)
self.CVS_Writter.writerow(self.CVS_Header)
def saveMeasurement(self, date, measurement):
self.CVS_Writter.writerow([date, measurement])

7
Software/DataAcquisition/hardware_connection.py → Software/DataAcquisition/physical_layer.py
Wyświetl plik

@ -1,7 +1,7 @@
from serial import Serial
class HardwareConnection:
class PhysicalLayer:
def __init__(self, config):
self.config = config
@ -14,6 +14,7 @@ class HardwareConnection:
self.serialPort.isOpen()
self.serialPort.flushInput()
def getMeasurement(self):
dataIn = self.serialPort.read(5)
def getData(self):
msgLength = 6
dataIn = self.serialPort.read(msgLength)
return dataIn

31
Software/DataAcquisition/state_machine.py
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@ -1,39 +1,40 @@
import datetime
from ionization_chamber import IonizationChamber
from application_layer import ApplicationLayer
from measurement_storage import MeasurementStorage
class IonizationChamberStateMachine:
def __init__(self, hardware):
self.hardware = hardware
def __init__(self, physicalLayer):
self.applicationLayer = ApplicationLayer(physicalLayer)
self.deviceMeasurement = 0.0
self.measurementStorage = MeasurementStorage()
self.nextState = self.initIonizationChamber
def tick(self):
self.nextState()
def initIonizationChamber(self):
self.chamber = IonizationChamber(self.hardware)
self.chamber.connect()
self.nextState = self.initOutputFile
self.applicationLayer.connect()
self.nextState = self.initMeasurementStorage
def initMeasurementStorage(self):
self.measurementStorage.connect()
def initOutputFile(self):
self.logFile = open('data.csv', 'w')
self.logFile.write("Time,Counter,DMM\n")
self.nextState = self.getMeasurementFromIonizationChamber
def getMeasurementFromIonizationChamber(self):
self.deviceMeasurement = self.chamber.getMeasurement()
self.deviceMeasurement = self.applicationLayer.getMeasurement()
self.nextState = self.saveMeasurement
def saveMeasurement(self):
now = datetime.datetime.now()
self.logFile.write("{0},{1}\n".format(
now, self.deviceMeasurement))
self.logFile.flush()
self.measurementStorage.saveMeasurement(now, self.deviceMeasurement)
self.nextState = self.showMeasurementToUser
def showMeasurementToUser(self):
print("{0}".format(self.deviceMeasurement))
self.nextState = self.getMeasurementFromIonizationChamber

23
Software/DataAcquisition/transport_layer.py 100644
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@ -0,0 +1,23 @@
class InvalidCRC(Exception):
pass
class MissingFrame(Exception):
pass
class InvalidMsgLength(Exception):
pass
class TransportLayer:
def __init__(self, physicalLayer):
self.physicalLayer = physicalLayer
def connect(self):
self.physicalLayer.connect()
def getFrame(self):
return self.physicalLayer.getData()

67
Software/Firmware/README.md
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@ -1,9 +1,60 @@
# Firmware
# Setting up development environment on Linux
* ["Data processing and firmware flashing" node architecture
](https://github.com/RobertGawron/IonizationChamber/wiki/%22Data-processing-and-firmware-flashing%22-node-architecture
)
* [Setting up development environment on Linux
](https://github.com/RobertGawron/IonizationChamber/wiki/Setting-up-development-environment-on-Linux)
* [Firmware compilation and hardware flashing
](https://github.com/RobertGawron/IonizationChamber/wiki/Firmware-compilation-and-hardware-flashing)
1. Install tools via apt-get:
```console
apt-get install screen git sdcc doxygen uncrustify libusb-1.0-0-dev python3-pip texlive-latex-base texlive-latex-extra texlive-extra-utils poppler-utils cmake cppcheck r-base-core shellcheck pdf2svg
```
Note: libusb is needed by stm8flash.
2. Clone, build and install stm8flash:
```console
git clone https://github.com/vdudouyt/stm8flash.git
cd stm8flash/
make
make install
```
3. Stm8flash enumerates as USB device, add access to this device for non-root users (so that its possible to flash the chip without being root):
```console
chmod o+w /dev/bus/usb/001/004
```
In above example, _/dev/bus/usb/001/004_ is where the stm8flash enumerates, you will get id of your stm8flash from error message when trying to flash the board.
# Firmware compilation and hardware flashing
## Initial configuration
Configure project using cmake, this step is needed only once.
In Software directory create build directory and go into it:
```
mkdir build
cd build
```
Run cmake:
```
cmake -DCMAKE_SYSTEM_NAME=Generic -DCMAKE_C_COMPILER=sdcc ../
```
## Compilation
Compilation is done using make in the directory where cmake files were generated (Software/Build)
```
make
```
Binary will be stored directory where makefile is.
# Hardware flashing
```
stm8flash -c stlink -p stm8s003f3 -w IonizationChamber.ihx
```

37
Software/README.md
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@ -1,5 +1,34 @@
# Software
## Architecture
* ["Data processing and firmware flashing" node architecture
](https://github.com/RobertGawron/IonizationChamber/wiki/%22Data-processing-and-firmware-flashing%22-node-architecture
)
Measurements are collected from COM port (tunneled over USB) by a python script and stored in .cvs file. This file can be later parsed using R scripts to to collect various diagrams (radioactivity changes over time, radioactivity histogram, box-plots for various samples).
<img src="../Documentation/Diagrams/HostArchitecture.svg" width="100%">
## Protocol for sending measurements via UART
## Purpose
To ensure data integrity sent from the ionization chamber device to computer, a simple protocol was added to encapsulate each data/command send.
## Protocol details
The field “msg length” describes amount of bytes the “data” section has.
Definition of the message:
<img src="../Documentation/Diagrams/UARTFrameFormat.svg" width="100%">
Content of data section in above message is an example and can be different depends on message id, but now only one message is supported and it is as shown above.
### Defined message ids and message content
* Msg id: 1 - data from last analog measurement of actual value.
* Msg data section:
* ADC configuration
* MSB (most significant byte) from ADC
* LSB (least significant byte) from ADC
### CRC
CRC is calculated xor’ing all bytes in "preamble" and "data" section.